Why You Are Nutrient Deficient Even When You Eat Well
This is one of the most common and frustrating things I see in clinic.
A client comes in with fatigue, brittle nails, hair that is thinning, headaches, or low mood. Their blood work shows they are deficient in iron, B12, vitamin D, zinc, or several of these at once. And when I ask about their diet, they are eating well. Genuinely well. Plenty of vegetables, good protein, minimal processed food.
So what is going on?
The truth is, getting enough of a nutrient from your food is only half of the equation. The other half is whether your body can actually absorb and use what you are eating. And that depends almost entirely on the health of your gut.
Digestion Is More Than What You Eat
When you eat a meal, your body has to break it down through a series of chemical and mechanical processes before any of its nutrients can be absorbed.
Stomach acid begins the process, breaking down proteins and killing pathogens. Digestive enzymes produced by the pancreas and the lining of the small intestine continue the work, converting food into the individual molecules the body can actually use. Proteins are broken down into amino acids. Carbohydrates become glucose. Fats are emulsified and absorbed through the gut lining into the lymphatic system.
The small intestine is where the majority of nutrient absorption happens. Its lining is covered in microscopic finger-like projections called villi, which dramatically increase the surface area available for absorption. When that lining is healthy, intact, and supported by the right microbial environment, absorption works well.
When it is not, even the most nutritious diet in the world cannot fully compensate.
What Gets in the Way of Absorption
Several conditions directly impair the small intestine's ability to absorb nutrients effectively.
SIBO, small intestinal bacterial overgrowth, is one of the most significant and most frequently missed. When bacteria that belong in the large intestine migrate into the small intestine, they interfere with the absorption process, damage the gut lining, and consume nutrients before the body can use them. B12 deficiency in particular is strongly associated with SIBO.
Coeliac disease causes an immune reaction to gluten that progressively damages the villi of the small intestine, reducing absorptive surface area and impairing the uptake of iron, folate, calcium, and B vitamins. Importantly, many people have non-coeliac gluten sensitivity that produces similar, though less severe, effects on the gut lining without a formal coeliac diagnosis.
IBS, while not a structural disease, is associated with altered gut motility, microbiome disruption, and intestinal permeability that collectively impair how efficiently nutrients are absorbed.
Beyond these specific conditions, the most common drivers of poor absorption in clinic are low stomach acid, which prevents proper protein breakdown and impairs the absorption of iron, B12, calcium, and zinc, low levels of digestive enzymes, gut dysbiosis where beneficial bacteria are depleted and less helpful species are dominant, and intestinal permeability, sometimes called leaky gut, where the tight junctions between gut lining cells break down and allow inflammatory compounds into the bloodstream while simultaneously impairing nutrient uptake.
The Factors That Make It Worse
Several everyday factors accelerate nutrient depletion and worsen absorption simultaneously.
Chronic stress is one of the most significant. Stress directly increases your body's requirements for vitamin C, magnesium, and B vitamins while simultaneously impairing digestion by suppressing stomach acid production and redirecting blood flow away from the gut. The result is a double burden where you need more and absorb less at exactly the same time. Irritability, fatigue, poor sleep, and low mood are often the first signs that these nutrients have become depleted.
Alcohol reduces the production of digestive enzymes in the gastrointestinal tract and impairs the absorption of B vitamins, zinc, folate, and magnesium. It also increases intestinal permeability, which is why people who drink regularly often experience reflux, bloating, and digestive discomfort alongside their nutritional deficiencies.
Certain medications including antidepressants, blood pressure medications, proton pump inhibitors, and the oral contraceptive pill all deplete specific nutrients as a known side effect. This is rarely discussed at the time of prescribing, but it matters clinically. Long-term use of the OCP, for example, is consistently associated with depletion of B6, B12, folate, zinc, and magnesium.
A diet high in sugar, refined carbohydrates, and ultra-processed foods drives gut dysbiosis, depletes the beneficial bacteria that support absorption, and creates an inflammatory gut environment that impairs nutrient uptake over time.
How Deficiencies Show Up in the Body
Your body gives clear signals when its nutrient reserves are running low.
Iron is often the first deficiency clients notice. It presents as fatigue that does not improve with rest, pale skin, brittle or ridged nails, cold hands and feet, headaches, dizziness, dry hair, and sometimes an inflamed or sore tongue. Women with heavy periods are particularly vulnerable to ongoing iron depletion.
B12 deficiency shows up as fatigue and low energy, neurological symptoms including tingling in the hands and feet, brain fog and memory difficulties, low mood, and in more significant deficiency, anaemia. It is strongly associated with low stomach acid, long-term PPI use, and veganism without appropriate supplementation.
Zinc deficiency presents as poor wound healing, white spots on the nails, hair loss, frequent infections, skin problems, and in women, hormonal disruption and irregular cycles.
Magnesium depletion, which is extremely common particularly in people under high stress, shows up as muscle cramps and tension, poor sleep, anxiety, headaches, constipation, and fatigue.
Vitamin D deficiency is associated with low mood, fatigue, poor immunity, bone pain, and muscle weakness. It is remarkably common in Australia despite the climate, largely because most people spend the majority of their day indoors.
The pattern across all of these is that deficiencies rarely appear alone. When one is present, others usually are too, because the same underlying gut issues that impair absorption of one nutrient tend to impair absorption of many.
What Actually Fixes It
Supplementing a deficiency without addressing why it developed rarely produces lasting results. The most important step is understanding the underlying reason absorption is impaired. That might mean investigating for SIBO, coeliac disease, or other conditions affecting the small intestine, assessing stomach acid and digestive enzyme function, testing the gut microbiome through functional stool testing, or reviewing medications and lifestyle factors that are driving depletion. Once the underlying driver is identified and addressed, nutrient levels respond much more predictably to dietary and supplementation support, and they stay up rather than repeatedly declining. This is the approach I take in clinic, and it produces very different results from simply prescribing iron or B12 and rechecking levels in three months. If you are eating well, supplementing, and still finding your levels do not hold, your gut is almost certainly part of the answer.
Working Together
If you have been dealing with persistent deficiencies that do not fully resolve despite a good diet and supplementation, getting a clear picture of what is happening in your gut is the most logical next step.
I see clients in person at my Spotswood clinic in Melbourne and via telehealth across Australia. A naturopathic consultation looks at your full picture, your diet, your health history, your current medications, and any relevant testing, and builds a plan that addresses the root cause rather than chasing individual markers.
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You can also read more about how I work on my conditions treated page or explore functional testing and what investigating your gut health looks like in practice.
Frequently Asked Questions About Nutrient Deficiencies and Gut Health
Can poor gut health really cause nutrient deficiencies even with a good diet? Yes, and this is one of the most important things to understand about nutrient deficiencies. Absorption happens in the gut, and if the gut lining is damaged, stomach acid is low, digestive enzymes are insufficient, or the microbiome is disrupted, even a genuinely nutritious diet cannot compensate. Addressing the gut is often what finally moves the needle when supplementation alone has not been effective.
How do I know if my nutrient deficiencies are gut-related? If your deficiencies are persistent despite supplementation, if you have multiple deficiencies rather than just one, if you have any digestive symptoms alongside your deficiencies, or if you have a history of antibiotic use, IBS, reflux, or bloating, gut function is almost certainly contributing. A comprehensive stool test and a review of digestive function gives a clear picture of where the impairment is occurring.
Does stress actually cause nutrient deficiencies? Yes, through two mechanisms simultaneously. Chronic stress increases your body's requirements for specific nutrients, particularly magnesium, vitamin C, and B vitamins, while also impairing digestion and absorption by suppressing stomach acid and reducing gut motility. The result is that stressed people tend to deplete nutrients faster and absorb them less efficiently at the same time.
Which medications are most likely to cause nutrient deficiencies? Proton pump inhibitors deplete B12, magnesium, calcium, and zinc. The oral contraceptive pill depletes B6, B12, folate, zinc, and magnesium. Metformin depletes B12. Long-term antidepressants can affect folate and B12. Blood pressure medications vary in their specific depletions. If you are on any long-term medication, it is worth asking a naturopath which nutrients may need monitoring and support.
Why do my iron levels keep dropping even when I supplement? Persistent iron deficiency despite supplementation almost always means either absorption is impaired, the underlying cause of depletion, such as heavy periods or ongoing blood loss, has not been addressed, or the supplement form is not well absorbed. Iron absorption is significantly impaired by low stomach acid, SIBO, coeliac disease, and gut inflammation. Getting your gut health properly assessed is usually what breaks the cycle.
Kylie Sartori is a degree-qualified naturopath based in Spotswood, Melbourne, specialising in gut health, microbiome restoration, hormonal health, and nutritional medicine. She offers in-person consultations at her Spotswood clinic and telehealth appointments for clients across Australia.
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